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On One Page

Quickview |

Gene |

Product(s) |

Expression|

Evolution |

References |

Quickview

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Standard Name	cdd
Gene Synonym(s)	ECK2136, b2143, JW2131^[1], JW2131
Product Desc.	Cdd^[2]^[3]; Component of CYTIDEAM-CPLX^[2] Cytidine deaminase; 2-deoxycytidine deaminase; mutants are 5-fluorodeoxycytidine resistant; binds Zn(II)^[4]
Product Synonyms(s)	cytidine/deoxycytidine deaminase^[1], B2143^[2]^[1], Cdd^[2]^[1] , ECK2136, JW2131, b2143
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): cdd^[2]
Regulation/Activity
Quick Links
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Notes

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Gene

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Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name	cdd
Mnemonic	CytiDine Deaminase
Synonyms	ECK2136, b2143, JW2131^[1], JW2131
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Notes

Location(s) and DNA Sequence

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<protect> See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Strain	Map location	Genome coordinates	Genome browsers	Sequence links
MG1655	48.06 minutes	MG1655: 2229866..2230750 <gbrowseImage> name=NC_000913:2229866..2230750 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2183082..2183966 <gbrowseImage> name=NC_012967:2183082..2183966 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2122349..2123233 <gbrowseImage> name=NC_012759:2122349..2123233 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2235178..2236062 <gbrowseImage> name=NC_007779:2235178..2236062 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2320874..2321758 <gbrowseImage> name=NC_010473:2320874..2321758 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
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Notes

Sequence Features

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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type	Strain	Genomic Location	Evidence	Reference	Notes
Coding Start (SO:0000323)	MG1655	2229866	Edman degradation	PMID:1567863 PMID:2692708 PMID:8506346 PMID:18482579
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Notes

Alleles and Phenotypes

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele	Nt change(s)	AA change(s)	Reference	Availability	Comments
Δcdd (Keio:JW2131)	deletion	deletion	PMID:16738554	Shigen CGSC9727^[5]
cdd::Tn5KAN-2 (FB20645)	Insertion at nt 656 in Plus orientation		PMID:15262929	E. coli Genome Project:FB20645	does not contain pKD46
cdd::Tn5KAN-2 (FB20646)	Insertion at nt 656 in Plus orientation		PMID:15262929	E. coli Genome Project:FB20646	contains pKD46
cdd-5				CGSC:7316
cdd-7				CGSC:7784
cdd-1				CGSC:9218
cdd-6				CGSC:12001
cdd-50				CGSC:23043
Δcdd-770::kan			PMID:16738554	CGSC:100270
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Notes

Genetic Interactions

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Interactor	Interaction	Allele	Score(s)	Reference(s)	Accessions	Notes
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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource	Resource Type	Source	Notes/Reference
JW2131	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCCATCCACGTTTTCAAACCGC Primer 2:CCAGCGAGAAGCACTCGGTCGAT
1E1	Kohara Phage	Genobase	PMID:3038334
2B2	Kohara Phage	Genobase	PMID:3038334
7F1	Kohara Phage	Genobase	PMID:3038334
7H12	Kohara Phage	Genobase	PMID:3038334
zbd-3104::Tn10	Linked marker	CAG12021 = CGSC7344^[5]	est. P1 cotransduction: 7% ^[6] Synonyms:zbc-3105::Tn10, zbd-3105::Tn10
napA722::Tn10	Linked marker	CAG12098 = CGSC7400^[5]	est. P1 cotransduction: 1% ^[6] Synonyms:zeg-722, zei-722::Tn10
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
EcoCyc	EcoCyc:EG10137	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10137	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000133	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946663	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0135	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007086	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Product(s)

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Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name	Cdd
Synonyms	cytidine/deoxycytidine deaminase^[1], B2143^[2]^[1], Cdd^[2]^[1] , ECK2136, JW2131, b2143
Product description	Cdd^[2]^[3]; Component of CYTIDEAM-CPLX^[2] Cytidine deaminase; 2-deoxycytidine deaminase; mutants are 5-fluorodeoxycytidine resistant; binds Zn(II)^[4]
EC number (for enzymes)	3.5.4.5^[1]
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Notes

Function

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<protect> Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier	GO ID	GO term name	Reference	Evidence Code	with/from	Aspect	Notes	Status
	GO:0005737	cytoplasm				C	Seeded from Riley et al 2006 ^[1].	Missing: evidence, reference
	GO:0001884	pyrimidine nucleoside binding	PMID:3910086	IDA: Inferred from Direct Assay		F	Seeded from EcoCyc (v14.0)	complete
	GO:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016193	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004126	cytidine deaminase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01558	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004126	cytidine deaminase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006263	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008270	zinc ion binding	PMID:8289286	IDA: Inferred from Direct Assay		F		complete
	GO:0004126	cytidine deaminase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR013171	F	Seeded from EcoCyc (v14.0)	complete
	GO:0001884	pyrimidine nucleoside binding	PMID:3910086	IDA: Inferred from Direct Assay		F	cytidine binding	complete
	GO:0004126	cytidine deaminase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR020797	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004126	cytidine deaminase activity	PMID:4944311	IDA: Inferred from Direct Assay		F		complete
	GO:0004126	cytidine deaminase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:3.5.4.5	F	Seeded from EcoCyc (v14.0)	complete
	GO:0015949	nucleobase, nucleoside and nucleotide interconversion	PMID:4944311	IDA: Inferred from Direct Assay		P		complete
	GO:0005829	cytosol	PMID:16858726	IDA: Inferred from Direct Assay		C	Seeded from EcoCyc (v14.0)	complete
	GO:0015949	nucleobase, nucleoside and nucleotide interconversion	PMID:4944312	IDA: Inferred from Direct Assay		P		complete
	GO:0008270	zinc ion binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002125	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008270	zinc ion binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006263	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008270	zinc ion binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR013171	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008270	zinc ion binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016192	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008270	zinc ion binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR020797	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008270	zinc ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0862	F	Seeded from EcoCyc (v14.0)	complete
	GO:0046087	cytidine metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006263	P	Seeded from EcoCyc (v14.0)	complete
	GO:0046087	cytidine metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR020797	P	Seeded from EcoCyc (v14.0)	complete
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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type	Partner	Notes	References	Evidence
Protein	Subunits of CYTIDEAM-CPLX	could be indirect
RNA	cytidine	substrate	PMID:4944311	kinetic assay
RNA	N4-methylcytidine	substrate	PMID:4944311	kinetic assay
RNA	3,4,5,6-tetrahydrouridine	inhibitor	PMID:4944311	kinetic assay
RNA	5,6-dihydrouridine	inhibitor	PMID:4944311	kinetic assay
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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment	Description	Evidence	Reference/Source	Notes
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Notes

Structure and Physical Properties

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<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence	at EcoCyc MHPRFQTAFA QLADNLQSAL EPILADKYFP ALLTGEQVSS LKSATGLDED ALAFALLPLA AACARTPLSN FNVGAIARGV SGTWYFGANM EFIGATMQQT VHAEQSAISH AWLSGEKALA AITVNYTPCG HCRQFMNELN SGLDLRIHLP GREAHALRDY LPDAFGPKDL EIKTLLMDEQ DHGYALTGDA LSQAAIAAAN RSHMPYSKSP SGVALECKDG RIFSGSYAEN AAFNPTLPPL QGALILLNLK GYDYPDIQRA VLAEKADAPL IQWDATSATL KALGCHSIDR VLLA
Length	294
Mol. Wt	31.54 kDa
pI	5.6 (calculated)
Extinction coefficient	29,910 - 30,535 (calc based on 9 Y, 3 W, and 5 C residues)
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Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type	Residues	Description	References
Domain	47..143	PF00383 Cytidine and deoxycytidylate deaminase zinc-binding region	PMID:19920124
Domain	157..279	PF08211 Cytidine and deoxycytidylate deaminase zinc-binding region	PMID:19920124
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<motif_map/>

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=cdd taxon=562,83333 </beststructure>

Models

View models at:

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</protect>

Structure figures

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Notes

Physical properties and substrate/inhibitor binding/kinetic information may be found in ^[7] and ^[8]
Crystal structure information may be found in ^[9]

Gene Product Resources

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Resource type	Source	Notes/Reference
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
NCBI (Protein) (EcoliWiki Page)	GI:16130081	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946663	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007086	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0ABF6	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10137	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10137	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946663	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000133	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0135	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Expression

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Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Cellular Levels

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See Help:Cellular levels

Molecule	Organism or Strain	Value	Units	Experimental Conditions	Assay used	Reference(s)
Protein	E. coli K-12 MC4100	9.15E+02	molecules/cell	Medium: median data from rich and minimal media Temperature (°C): 37 Doubling time (min): Growth Rate(min): Growth phase: other:	emPAI	PMID:18304323
Protein	E. coli K-12 MG1655	313	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
Protein	E. coli K-12 MG1655	287	molecules/cell/generation	Medium: MOPS Minimal Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
Protein	E. coli K-12 MG1655	320	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
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Notes

Transcription and Transcriptional Regulation

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See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)
cdd
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Figure courtesy of RegulonDB

</protect>

Notes

This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Translation and Regulation of Translation

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<protect><gbrowseImage> name=NC_000913:2229846..2229886 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

</protect>

Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

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Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental

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<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name	Mutation	Phenotype	Reference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type	Reference	Notes
microarray	GEO Profiles:b2143 (EcoliWiki Page)	NCBI GEO profiles for cdd
microarray	GenExpDB:b2143 (EcoliWiki Page)	Summary of data for cdd from multiple microarray studies
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Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name	Resource Type	Description	Source	Notes
	GFP Fusion	Intergenic region (2229655..2229870) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ05; Well:A10^[10]
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Notes

Accessions Related to cdd Expression

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
EcoCyc	EcoCyc:EG10137	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0135	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2143
EcoGene	EcoGene:EG10137	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000133	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007086	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Evolution

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Homologs in Other Organisms

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See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism	Homologs (Statistics)	Comments
Arabidopsis thaliana	AT2G19570 (score: 1.000; bootstrap: 100%) AT4G29610 (score: 0.361) AT4G29600 (score: 0.306) AT4G29620 (score: 0.225) AT4G29640 (score: 0.199) AT4G29570 (score: 0.149) AT4G29650 (score: 0.114) AT4G29630 (score: 0.088) AT4G29580 (score: 0.074)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000008074 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-040426-1911 (score: 1.000; bootstrap: 100%) ZDB-CDNA-040425-2851 (score: 1.000; bootstrap: 100%) ZDB-CDNA-041114-88 (score: 0.365) ZDB-GENE-041114-88 (score: 0.365)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0032001 (score: 1.000; bootstrap: 100%) FBgn0032002 (score: 0.369) FBgn0032003 (score: 0.280)	From Inparanoid:20070104
Homo sapiens	ENSP00000289839 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Mus musculus	MGI:1919519 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000000499 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPAC15564c (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	CDD	From SHIGELLACYC
E. coli O157	CDD	From ECOO157CYC
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Do-It-Yourself Web Tools

Notes

Families

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
Pfam (EcoliWiki Page)	PF00383 Cytidine and deoxycytidylate deaminase zinc-binding region
Panther (EcoliWiki Page)	PTHR11644:SF12
Superfamily (EcoliWiki Page)	SUPERFAMILY:53927
Superfamily (EcoliWiki Page)	SUPERFAMILY:53927
Pfam (EcoliWiki Page)	PF08211 Cytidine and deoxycytidylate deaminase zinc-binding region
EcoCyc	EcoCyc:EG10137	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10137	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000133	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0135	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007086	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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References

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See Help:References for how to manage references in EcoliWiki.

↑ ^1.0 ^1.1 ^1.2 ^1.3 ^1.4 ^1.5 ^1.6 ^1.7 ^1.8 ^1.9 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.0 ^2.1 ^2.2 ^2.3 ^2.4 ^2.5 ^2.6 ^2.7 ^2.8 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^5.0 ^5.1 ^5.2 CGSC: The Coli Genetics Stock Center
↑ ^6.0 ^6.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).
↑ Vita, A et al. (1985) Cytidine deaminase from Escherichia coli B. Purification and enzymatic and molecular properties. Biochemistry 24 6020-4 PubMed
↑ Cohen, RM & Wolfenden, R (1971) Cytidine deaminase from Escherichia coli. Purification, properties and inhibition by the potential transition state analog 3,4,5,6-tetrahydrouridine. J. Biol. Chem. 246 7561-5 PubMed
↑ Betts, L et al. (1994) Cytidine deaminase. The 2.3 A crystal structure of an enzyme: transition-state analog complex. J. Mol. Biol. 235 635-56 PubMed
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

cdd:On One Page

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Notes

Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Interactions

Notes

Genetic Resources

Notes

Accessions in Other Databases

Notes

Links

Product(s)

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

Expression

Overview

Cellular Levels

Notes

Transcription and Transcriptional Regulation

Notes

Translation and Regulation of Translation

Notes

Turnover and Regulation of Turnover

Notes

Experimental

Notes

Accessions Related to cdd Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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